diff --git a/core/src/main/scala/eu/nomad_lab/h5/ArchiveH5.scala b/core/src/main/scala/eu/nomad_lab/h5/ArchiveH5.scala
index a605a7b2d46bca0a7f36e7f575054b2e41baa4f8..2f6ddc84698ec3371cfc117e344765e0eb295c44 100644
--- a/core/src/main/scala/eu/nomad_lab/h5/ArchiveH5.scala
+++ b/core/src/main/scala/eu/nomad_lab/h5/ArchiveH5.scala
@@ -1,6 +1,13 @@
package eu.nomad_lab.h5
import eu.nomad_lab.{ H5Lib, RefCount }
+import hdf.hdf5lib.{ H5, HDF5Constants }
+
+case class GroupObjectInfoH5(
+ oname: String,
+ otype: Int,
+ orefs: Long
+)
/**
* represents an archive in an hdf5 file
@@ -19,6 +26,16 @@ class ArchiveH5(
H5Lib.groupClose(archiveGroup)
fileH5.release()
}
+
+ protected var calcRemaining: Int = 0
+ protected var cursor: Int = 0
+ val count = if (archiveGroup >= 0) H5.H5Gn_members(archiveGroup, "/").toInt else 0
+ protected var childNames: Array[String] = new Array[String](count)
+ protected var childTypes: Array[Int] = new Array[Int](count)
+ protected var lTypes: Array[Int] = new Array[Int](count)
+ protected var childRefs: Array[Long] = new Array[Long](count)
+ protected var currentCalc: Option[CalculationH5] = None
+
val archiveRef = this
/**
* returns a calculation with the given gid if contained in this archive
@@ -30,4 +47,48 @@ class ArchiveH5(
calculationGroup = H5Lib.groupGet(archiveGroup, calculationGid, false)
)
}
+ def closeLastCalculation() = {
+ currentCalc match {
+ case None => ()
+ case Some(calc) =>
+ H5Lib.groupClose(calc.calculationGroup)
+ }
+ }
+
+ if (archiveGroup >= 0) {
+ H5.H5Gget_obj_info_all(archiveGroup, "/", childNames, childTypes, lTypes, childRefs, HDF5Constants.H5_INDEX_NAME)
+ calcRemaining = childNames.length
+ }
+
+ def iterator: Iterator[CalculationH5] = new Iterator[CalculationH5] {
+
+ override def hasNext: Boolean = if (calcRemaining > 0) true else false
+
+ override def next(): CalculationH5 = {
+ closeLastCalculation()
+ if (hasNext) {
+ currentCalc = Some(new CalculationH5(
+ archive = archiveRef,
+ calculationGid = childNames(cursor),
+ calculationGroup = H5Lib.groupGet(archiveGroup, childNames(cursor), false)
+ ))
+ calcRemaining -= 1
+ cursor += 1
+ currentCalc.get
+ } else
+ throw new java.util.NoSuchElementException("Next on empty iterator")
+ }
+ }
+
+// def visit():org.json4s.JValue = {
+// val itr = iterator
+// var res = org.json4s.JObject()
+// itr foreach( c => res = res + c.visit)
+// }
}
+/* override def apply(idx: Int): CalculationH5 = {
+ new CalculationH5( archive = archiveRef,
+ calculationGid = oname(idx),
+ calculationGroup = H5Lib.groupOpen(archiveGroup,oname(idx))
+ )
+ }*/
\ No newline at end of file
diff --git a/core/src/main/scala/eu/nomad_lab/h5/CalculationH5.scala b/core/src/main/scala/eu/nomad_lab/h5/CalculationH5.scala
index 50459c36eb57561b51cdfcc3fd324f5bd70eb4ab..ea7bf50012888ba4e0d30d99d3ed16701f329048 100644
--- a/core/src/main/scala/eu/nomad_lab/h5/CalculationH5.scala
+++ b/core/src/main/scala/eu/nomad_lab/h5/CalculationH5.scala
@@ -7,7 +7,7 @@ import eu.nomad_lab.JsonUtils
import eu.nomad_lab.meta.KnownMetaInfoEnvs
import eu.nomad_lab.meta.MetaInfoEnv
import eu.nomad_lab.meta.MetaInfoRecord
-
+import org.json4s.{ JArray, JBool, JDecimal, JDouble, JField, JInt, JNothing, JNull, JObject, JString, JValue }
import scala.collection.mutable
object CalculationH5 {
@@ -36,6 +36,7 @@ class CalculationH5(
val sectionTables0: Map[String, SectionTableH5] = Map(),
val valueTables0: Map[String, ValueTableH5] = Map()
) extends RefCount {
+
archive.retain()
def metaInfoEnv: MetaInfoEnv = {
@@ -121,7 +122,11 @@ class CalculationH5(
}
}
}
-
+// def visit: JValue = {
+// JObject(
+// JField("calculationGid",JString(calculationGid) )::Nil
+// )
+// }
/**
* clears the value table cache
*/
diff --git a/core/src/main/scala/eu/nomad_lab/h5/Section.scala b/core/src/main/scala/eu/nomad_lab/h5/Section.scala
index cf66652db7b808798e5c702b4ab4feb65133d121..270058c4d4c8a3712cb099d14e08aa056a5eddaf 100644
--- a/core/src/main/scala/eu/nomad_lab/h5/Section.scala
+++ b/core/src/main/scala/eu/nomad_lab/h5/Section.scala
@@ -245,7 +245,7 @@ class SectionCollectionH5(
/**
* gIndex of the last section in this collection (inclusive)
*
- * If there are no entires then upperGIndex < lowerGIndex
+ * If there are no entries then upperGIndex < lowerGIndex
*/
val upperGIndex: Long = upperGIndex0 match {
case Some(i) => i
@@ -267,7 +267,7 @@ class SectionCollectionH5(
/**
* gIndex of the first section in this collection (inclusive)
*
- * If there are no entires then upperGIndex < lowerGIndex
+ * If there are no entries then upperGIndex < lowerGIndex
*/
var lowerGIndex: Long = lowerGIndex0 match {
case Some(i) => i
diff --git a/core/src/main/scala/eu/nomad_lab/h5/Value.scala b/core/src/main/scala/eu/nomad_lab/h5/Value.scala
index 2ccbe27dbfda0ffcd86012613b4a84fa30e01237..0f8f8791d9490bae64d8b8f86711e4aba3a57469 100644
--- a/core/src/main/scala/eu/nomad_lab/h5/Value.scala
+++ b/core/src/main/scala/eu/nomad_lab/h5/Value.scala
@@ -859,7 +859,7 @@ abstract class ValueArrayH5[T <: NArray](
}
}
- override def arrayValue(valueOffset: Seq[Long] = Seq(), valueDims: Seq[Long] = Seq()): T;
+ override def arrayValue(valueOffset: Seq[Long] = Seq(), valueDims: Seq[Long] = Seq()): T
def jValue: jn.JValue = {
val shape = arrayShape
diff --git a/core/src/test/scala/eu/nomad_lab/h5/FileH5Spec.scala b/core/src/test/scala/eu/nomad_lab/h5/FileH5Spec.scala
index 38839b586cf7ec3d14f24a7e71c2b281b4e95dce..2a490a04bbf9505504586a787cb2160fac6a0530 100644
--- a/core/src/test/scala/eu/nomad_lab/h5/FileH5Spec.scala
+++ b/core/src/test/scala/eu/nomad_lab/h5/FileH5Spec.scala
@@ -8,18 +8,26 @@ object FileH5Spec extends Specification {
skipAllUnless(H5Lib.readSupport)
"h5Tests" >> {
- val fileH5 = FileH5(filePath = Paths.get("src/test/resources/testMetaInfoCompiler/P0Hx_S10YdRE_zQvqKyvYWSPw_pyK.h5"))
- val archiveH5 = fileH5.archive("RseHEMpz-OaPkanAHPxea8srdAPjh")
- val calculation = archiveH5.calculation("C0Hx_S10YdRE_zQvqKyvYWSPw_pyK")
- val section_run: SectionTableH5 = calculation.sectionTable("section_run")
- val firstRun = section_run(0)
- val singleConfTable = firstRun.table.subSectionTable("section_single_configuration_calculation")
- val firstConf = singleConfTable(0)
- val energies = firstConf.table.subValueTable("energy_total")
- val energy = energies(0)
- "energy" >> {
- energy.isEmpty must_== (false)
+ "should be able to read the energy value stored in HDF5 file" >> {
+ val fileH5 = FileH5(filePath = Paths.get("src/test/resources/testMetaInfoCompiler/P0Hx_S10YdRE_zQvqKyvYWSPw_pyK.h5"))
+ val archiveH5 = fileH5.archive("RseHEMpz-OaPkanAHPxea8srdAPjh")
+ val calculation = archiveH5.calculation("C0Hx_S10YdRE_zQvqKyvYWSPw_pyK")
+ val section_run: SectionTableH5 = calculation.sectionTable("section_run")
+ val firstRun = section_run(0)
+ val singleConfTable = section_run.subSectionTable("section_single_configuration_calculation")
+ val firstConf = singleConfTable(0)
+ val energies = singleConfTable.subValueTable("energy_total")
+ val (datasetName, datasetId) = energies.openValueDataset(Seq(1))
+ val v = energies.valueGetLocal(datasetId, 0)
+// println(v)
+ singleConfTable.closeSectionGroup()
+ section_run.isEmpty must_== false
+ firstRun.isEmpty must_== false
+ firstConf.isEmpty must_== false
+ energies.isEmpty must_== false
+ v.getDouble(0) == -1.6605525795476488E-13 must_== true
+
}
}